Setup North American Trawl Data

library(data.table)
library(ggplot2)

Download data from Ocean Adapt

trawl <- readRDS(url('https://raw.githubusercontent.com/pinskylab/OceanAdapt/master/data_clean/all-regions-full.rds'))
trawl <- data.table(trawl)

Plot taxa by region by year to look for taxa that aren’t recorded consistently

sppbyyr <- trawl[, .(pres = length(spp)), by = .(region, year, spp)]
regs <- sppbyyr[, sort(unique(region))]

# loop through each region and make a plot
for(i in 1:length(regs)){
  p1 <- ggplot(sppbyyr[region == regs[i]], aes(x = year, y = spp, group = spp)) +
    geom_line(size = 0.2) +
    geom_point(size = 0.2) +
    theme(text=element_text(size = 3), 
          axis.text.x = element_text(angle = 90),
          strip.text.x = element_text(size = 5)) +
    ggtitle(regs[i])
  print(p1)
}

Trim out species not recorded consistently

Save out

save(trawl, file = "data/NE_trawl_data_full.Rdata")